Contacts of the helix formed by residues 192 - 203 (chain B) in PDB entry 3L2W
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B THR* 2.8 30.8 + - - +
188B ALA 3.3 11.1 + - - -
190B PHE 3.3 1.7 - - - +
191B THR* 1.3 82.4 - - - +
193B SER* 1.3 59.3 + - - +
194B THR* 3.6 5.0 + - - -
195B PHE* 3.1 20.1 + - - +
196B ALA* 3.0 21.3 + - - +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B THR 3.7 1.0 + - - -
192B SER* 1.3 72.7 - - - +
194B THR* 1.3 61.8 + - - +
196B ALA* 3.4 9.8 - - - +
197B GLU* 2.8 30.3 + - - +
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B THR* 4.0 18.2 - - + -
167B VAL* 5.5 4.9 - - + -
192B SER* 3.3 3.6 + - - -
193B SER* 1.3 77.8 + - - +
195B PHE* 1.3 64.4 + - - +
197B GLU* 3.4 5.6 + - - +
198B TRP* 3.0 22.6 + - - +
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Residues in contact with PHE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE* 4.3 11.2 - - + -
163B THR* 3.6 11.1 - - + +
166B THR* 3.4 28.7 - - + -
167B VAL* 4.0 19.1 - - + -
170B LEU* 3.9 23.1 - - + -
182B ILE* 4.4 5.4 - - + -
184B SER* 5.8 0.7 - - - -
189B ALA 3.9 9.0 - - - +
190B PHE* 3.4 29.8 - + + +
192B SER* 3.1 21.0 + - - +
194B THR* 1.3 73.4 - - - +
196B ALA* 1.3 66.8 + - - +
198B TRP* 3.1 25.8 + + - +
199B ALA* 3.0 22.3 + - - +
206B LEU* 3.7 29.2 - - + -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PHE 5.8 0.2 - - - +
191B THR 5.3 1.6 - - - +
192B SER 3.0 15.2 + - - +
193B SER* 3.4 15.3 - - - +
195B PHE* 1.3 77.6 - - - +
197B GLU* 1.3 61.3 + - - +
199B ALA* 3.3 3.8 + - - +
200B LYS* 3.1 21.0 + - - +
206B LEU* 4.2 16.0 - - + +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B SER 2.8 19.6 + - - +
194B THR* 3.8 6.1 - - + +
196B ALA* 1.3 69.1 - - - +
198B TRP* 1.3 67.5 + - - +
200B LYS* 2.9 9.2 + - - +
201B GLU* 2.9 33.3 + - - +
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Residues in contact with TRP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B VAL* 3.5 33.2 - - + +
170B LEU* 3.7 40.6 - - + -
171B ASN* 3.0 24.4 + - - -
174B THR* 4.2 8.7 - - + -
182B ILE* 3.9 15.7 - - + -
194B THR 3.0 14.5 + - - +
195B PHE* 3.2 26.5 - + - +
197B GLU* 1.3 75.5 - - - +
199B ALA* 1.3 78.9 + - + +
201B GLU* 3.4 7.5 + - - +
202B ARG* 2.8 68.2 + - - +
204B ILE* 3.7 28.7 - - + -
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B PHE 3.0 11.5 + - - +
196B ALA 3.7 7.9 - - - +
197B GLU 3.1 0.2 - - - -
198B TRP* 1.3 89.9 - - + +
200B LYS* 1.3 64.7 + - - +
202B ARG 3.3 2.0 + - - +
203B GLY 3.0 4.7 + - - -
204B ILE* 2.9 46.9 + - + +
206B LEU* 3.8 28.3 - - + -
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ALA 3.1 12.1 + - - +
197B GLU* 2.9 11.2 + - - +
199B ALA* 1.3 77.4 - - - +
201B GLU* 1.3 63.2 + - - +
203B GLY* 3.2 13.3 + - - +
204B ILE 4.4 3.1 + - - -
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B GLU* 2.9 19.5 + - - +
198B TRP* 3.4 9.6 + - - +
200B LYS* 1.3 76.8 - - - +
202B ARG* 1.3 90.9 + - - +
203B GLY* 3.2 1.2 + - - -
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ASN* 4.3 6.4 + - - +
171B ASN* 3.7 15.2 + - - +
174B THR* 4.4 12.4 + - - -
178B ILE* 4.1 24.9 - - + +
198B TRP* 2.8 80.1 + - - +
199B ALA 3.3 3.0 + - - +
201B GLU* 1.3 107.0 + - - +
203B GLY* 1.3 62.3 + - - +
204B ILE* 3.4 21.1 - - + +
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Residues in contact with GLY 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ASN* 2.8 25.2 + - - +
180B LYS 4.5 0.7 - - - +
199B ALA 3.0 4.1 + - - -
200B LYS* 3.2 8.5 + - - -
201B GLU 3.1 6.0 + - - -
202B ARG* 1.3 78.2 - - - +
204B ILE* 1.3 54.8 + - - +
205B HIS 4.1 0.9 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il